chr7-44152420-C-T

Position:

• chr7-44152420-C-T

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PS4 PP1_Strong PS3_Supporting PP4_Moderate PP2 PP3 PM2_Supporting

This summary comes from the ClinGen Evidence Repository: The c.214G>A variant in the glucokinase gene, GCK causes an amino acid change of glycine to arginine at codon 72 (p.(Gly72Arg)) of NM_000162.5. GCK is defined by the ClinGen MDEP as a gene that has a low rate of benign missense variation and has pathogenic missense variants as a common mechanism of disease (PP2). This variant is also predicted to be deleterious by computational evidence, with a REVEL score of 0.994, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant has an incomputable gnomAD v2.1.1 Popmax minor filtering allele frequency due to 0 copies in the European non-Finnish subpopulation and 1 copies in the African/African American subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (ENF Popmax FAF <= 0.000003 and <= 2 copies in ENF and <=1 copy in any other subpopulation) (PM2_Supporting). This variant was identified in 48 unrelated individuals with diabetes/hyperglycemia (PS4; internal lab contributors). This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and OGTT increment < 3 mmol/L) (PP4_Moderate, internal lab contributors). This variant segregated with diabetes/hyperglycemia with 23 informative meioses in multiple families (PP1_Strong; internal lab contributors). A kinetic analysis of recombinant wild-type (WT) and mutant glucokinase demonstrated that the wild-type kinetic parameters passed the quality control, the wild-type ATP Km was between 0.4-0.65, the p.Gly72Arg had a relative activity index (RAI) > 0.5 and a relative stability index (RSI) <=0.5 (PS3_Supporting; PMID:25015100). In summary, c.214G>A meets the criteria to be classified as Pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (specification version 1.2.0, approved 8/11/2023): PS4, PP1_Strong, PP4_Moderate, PS3_Supporting, PM2_Supporting, PP3, PP2. LINK:https://erepo.genome.network/evrepo/ui/classification/CA213771/MONDO:0015967/086

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: GCK ENST00000403799.8 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:10
• Conservation: PhyloP100: 7.90

Genes affected

GCK (HGNC:4195): (glucokinase) This gene encodes a member of the hexokinase family of proteins. Hexokinases phosphorylate glucose to produce glucose-6-phosphate, the first step in most glucose metabolism pathways. In contrast to other forms of hexokinase, this enzyme is not inhibited by its product glucose-6-phosphate but remains active while glucose is abundant. The use of multiple promoters and alternative splicing of this gene result in distinct protein isoforms that exhibit tissue-specific expression in the pancreas and liver. In the pancreas, this enzyme plays a role in glucose-stimulated insulin secretion, while in the liver, this enzyme is important in glucose uptake and conversion to glycogen. Mutations in this gene that alter enzyme activity have been associated with multiple types of diabetes and hyperinsulinemic hypoglycemia. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Pathogenic. Variant got 14 ACMG points.

• PS3: For more information check the summary or visit ClinGen Evidence Repository.
• PS4: For more information check the summary or visit ClinGen Evidence Repository.
• PM2: For more information check the summary or visit ClinGen Evidence Repository.
• PP1: For more information check the summary or visit ClinGen Evidence Repository.
• PP2: For more information check the summary or visit ClinGen Evidence Repository.
• PP3: For more information check the summary or visit ClinGen Evidence Repository.
• PP4: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GCK	NM_000162.5	c.214G>A	p.Gly72Arg	missense_variant	3/10	ENST00000403799.8	NP_000153.1
GCK	NM_033507.3	c.217G>A	p.Gly73Arg	missense_variant	3/10		NP_277042.1
GCK	NM_033508.3	c.211G>A	p.Gly71Arg	missense_variant	4/11		NP_277043.1
GCK	NM_001354800.1	c.214G>A	p.Gly72Arg	missense_variant	3/11		NP_001341729.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GCK	ENST00000403799.8	c.214G>A	p.Gly72Arg	missense_variant	3/10	1	NM_000162.5	ENSP00000384247	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.00000398 AC: 1 AN: 251364 Hom.: 0 AF XY: 0.00000736 AC XY: 1 AN XY: 135888

Gnomad AFR exome AF: 0.0000615

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461876 Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1 AN XY: 727240

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

Bravo AF: 0.00000756

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000116 AC: 1

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:10

Revision: reviewed by expert panel

Submissions by phenotype

not provided Pathogenic:5

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Apr 04, 2024	Published functional studies demonstrate increased activity compared to wild type as well as decreased thermal stability of the protein (Sagen et al., 2006; Raimondo et al., 2014); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Not observed at significant frequency in large population cohorts (gnomAD); Missense variants in this gene are a common cause of disease and they are underrepresented in the general population; This variant is associated with the following publications: (PMID: 17389332, 18399931, 24735133, 29056535, 34462253, 31216263, 21831042, 19187021, 16731834, 25015100, 24411943, 26669242, 12442280, 12955723, 20337973, 17573900, 10447526, 30191644, 30663027, 34108472, 33565752, 34746319) -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jul 12, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital	Jul 10, 2020	The p.Gly72Arg variant substitutes the glycine with arginine at position 72 of the protein. This is a recurrent pathogenic variant that has been reported in the heterozygous state in multiple individuals with MODY (PMID: 19790256, PMID: 10447526, PMID: 12442280, PMID: 30191644 and others). This is not a common variant in the general population (observed in 1 of 251,364 alleles; gnomAD v2.1.1). The p.Gly72Arg variant has been experimentally demonstrated to reduce GCK catalytic activity (PMID: 19187021, PMID: 17389332) -
Likely pathogenic, criteria provided, single submitter	clinical testing	AiLife Diagnostics, AiLife Diagnostics	Dec 01, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 15, 2023	This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 72 of the GCK protein (p.Gly72Arg). This variant is present in population databases (rs193922289, gnomAD 0.007%). This missense change has been observed in individuals with autosomal dominant maturity-onset diabetes of the young (PMID: 10447526, 12442280, 30259503, 30447144, 30663027, 31216263; Invitae). ClinVar contains an entry for this variant (Variation ID: 36209). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt GCK protein function. Studies have shown that this missense change alters GCK gene expression (PMID: 16731834, 17389332). This variant disrupts the p.Gly72 amino acid residue in GCK. Other variant(s) that disrupt this residue have been observed in individuals with GCK-related conditions (PMID: 31216263), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic. -

Monogenic diabetes Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jun 17, 2022	Variant summary: GCK c.214G>A (p.Gly72Arg) results in a non-conservative amino acid change located in the Hexokinase, N-terminal domain (IPR022672) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 4e-06 in 251464 control chromosomes. c.214G>A has been reported in the literature in multiple individuals affected with Maturity Onset Diabetes Of The Young 2 (example, Mantovani_2003, Lehto_1999, Cao_2002, Pruhova_2010). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -
Pathogenic, reviewed by expert panel	curation	ClinGen Monogenic Diabetes Variant Curation Expert Panel	Aug 13, 2023	The c.214G>A variant in the glucokinase gene, GCK causes an amino acid change of glycine to arginine at codon 72 (p.(Gly72Arg)) of NM_000162.5. GCK is defined by the ClinGen MDEP as a gene that has a low rate of benign missense variation and has pathogenic missense variants as a common mechanism of disease (PP2). This variant is also predicted to be deleterious by computational evidence, with a REVEL score of 0.994, which is greater than the MDEP VCEP threshold of 0.70 (PP3). This variant has an incomputable gnomAD v2.1.1 Popmax minor filtering allele frequency due to 0 copies in the European non-Finnish subpopulation and 1 copies in the African/African American subpopulation, thereby meeting the ClinGen MDEP threshold criteria for PM2_Supporting (ENF Popmax FAF <= 0.000003 and <= 2 copies in ENF and <=1 copy in any other subpopulation) (PM2_Supporting). This variant was identified in 48 unrelated individuals with diabetes/hyperglycemia (PS4; internal lab contributors). This variant was identified in an individual with a clinical history highly specific for GCK-hyperglycemia (FBG 5.5-8 mmol/L and HbA1c 5.6 - 7.6% and OGTT increment < 3 mmol/L) (PP4_Moderate, internal lab contributors). This variant segregated with diabetes/hyperglycemia with 23 informative meioses in multiple families (PP1_Strong; internal lab contributors). A kinetic analysis of recombinant wild-type (WT) and mutant glucokinase demonstrated that the wild-type kinetic parameters passed the quality control, the wild-type ATP Km was between 0.4-0.65, the p.Gly72Arg had a relative activity index (RAI) > 0.5 and a relative stability index (RSI) <=0.5 (PS3_Supporting; PMID: 25015100). In summary, c.214G>A meets the criteria to be classified as Pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP VCEP (specification version 1.2.0, approved 8/11/2023): PS4, PP1_Strong, PP4_Moderate, PS3_Supporting, PM2_Supporting, PP3, PP2. -
Likely pathogenic, criteria provided, single submitter	curation	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Jan 22, 2020	The p.Gly72Arg variant in GCK has been reported in at least 12 individuals (including 2 Mediterranean, 2 Scandinavian, 2 Spanish, 1 Italian, 1 Czech, 1 Turkish, 1 Slovakian, 1 Norwegian, and 1 Asian individuals) with Monogenic Diabetes, segregated with disease in 6 affected relatives from 3 families (PMID: 27106716, 25015100, 22493702, 18399931, 10447526, 12955723, 20337973, 17573900, 15305805), and has been identified in 0.006155% (1/16248) of African chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs193922289). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a carrier frequency. Please note that for diseases with clinical variability, or reduced penetrance, pathogenic variants may be present at a low frequency in the general population. This variant has also been reported pathogenic in ClinVar (Variation ID: 36209). In vitro functional studies provide some evidence that the p.Gly72Arg variant may impact protein activity and interactions with a regulatory protein (PMID: 21831042, 22028181, 17389332, 19187021). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. The p.Gly72Arg is located in a region of GCK that is essential to ATP binding and associated with hypoglycemia, suggesting that this variant is in an important functional domain and slightly supports pathogenicity (PMID: 15305805, 19187021). In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic. ACMG/AMP Criteria applied: PS3_moderate, PS4_Moderate, PP1_Moderate, PM2_Supporting, PP3, PM1_Supporting (Richards 2015). -

Maturity-onset diabetes of the young type 2 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Cardiovascular Genetics Laboratory, PathWest Laboratory Medicine WA - Fiona Stanley Hospital

Jan 31, 2022

The GCK p.Gly72Arg variant is pathogenic for maturity-onset diabetes of the young (MODY), with functional studies demonstrating that Gly27Arg results in reduced glucokinase activity and loss of stabilising interactions with glucokinase regulatory protein (PMID: 19187021, 17389332). -

Maturity onset diabetes mellitus in young Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 13, 2020

The p.G72R variant (also known as c.214G>A), located in coding exon 3 of the GCK gene, results from a G to A substitution at nucleotide position 214. The glycine at codon 72 is replaced by arginine, an amino acid with dissimilar properties. This variant has been identified in numerous maturity onset diabetes of the young families (Lehto M et al. Diabetologia, 1999 Sep;42:1131-7; Cao H et al. Hum. Mutat., 2002 Dec;20:478-9; Mantovani V et al. Hum. Mutat., 2003 Oct;22:338; Sagen JV et al. Pediatr Diabetes, 2008 Oct;9:442-9; Pruhova S et al. Pediatr Diabetes, 2010 Dec;11:529-35; Valentínová L et al. PLoS ONE, 2012 May;7:e34541; Raimondo A et al. Hum. Mol. Genet., 2014 Dec;23:6432-40; Bansal V et al. BMC Med, 2017 12;15:213). In addition, kinetic studies demonstrated reduced thermal stability compared to wild type (Raimondo A et al. Hum. Mol. Genet., 2014 Dec;23:6432-40). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.44	D
BayesDel_noAF	Pathogenic	0.58
CADD	Pathogenic	32
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.98	.;D;.;.;.
Eigen	Pathogenic	0.97
Eigen_PC	Pathogenic	0.86
FATHMM_MKL	Uncertain	0.95	D
LIST_S2	Pathogenic	1.0	D;D;.;D;D
M_CAP	Pathogenic	0.85	D
MetaRNN	Pathogenic	0.98	D;D;D;D;D
MetaSVM	Pathogenic	0.95	D
MutationAssessor	Pathogenic	4.2	.;H;.;.;.
MutationTaster	Benign	1.0	A;A;A;A
PrimateAI	Pathogenic	0.91	D
PROVEAN	Pathogenic	-7.8	.;D;D;D;D
REVEL	Pathogenic	0.99
Sift	Pathogenic	0.0	.;D;D;D;D
Sift4G	Pathogenic	0.0	D;D;D;D;D
Polyphen		1.0	D;D;D;D;.
Vest4		0.97
MutPred		0.99		.;Loss of sheet (P = 0.1398);.;.;Loss of sheet (P = 0.1398);
MVP		0.97
MPC		2.4
ClinPred		1.0	D
GERP RS		4.7
Varity_R		0.98
gMVP		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs193922289; hg19: chr7-44192019;